Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.
Nils Grabole, Jitao David Zhang, Stefan Aigner, Nadine Ruderisch, Veronica Costa, Felix C Weber, Michel Theron, Nikolaos Berntenis, Olivia Spleiss, Martin Ebeling, Gene W Yeo, Ravi Jagasia, Anna Kiialainen
Genome medicine · 2016 · Vol. 8 (1) · pp. 94
Abstract
Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology and suggest new targets for treatment. We investigate the disease phenotype of TSC by neural differentiation of a human stem cell model that had been deleted for TSC2 by genome editing. Comprehensive genomic analysis was performed by RNA sequencing and ribosome profiling to obtain a detailed genome-wide description of alterations on both the transcriptional and translational level. The molecular effect of mTOR inhibitors used in the clinic was monitored and comparison to published data from patient biopsies and mouse models highlights key pathogenic processes. TSC2-deficient neural stem cells showed severely reduced neuronal maturation and characteristics of astrogliosis instead. Transcriptome analysis indicated an active inflammatory response and increased metabolic activity, whereas at the level of translation ribosomal transcripts showed a 5'UTR motif-mediated increase in ribosome occupancy. Further, we observed enhanced protein synthesis rates of angiogenic growth factors. Treatment with mTOR inhibitors corrected translational alterations but transcriptional dysfunction persisted. Our results extend the understanding of the molecular pathophysiology of TSC brain lesions, and suggest phenotype-tailored pharmacological treatment strategies.
Linked datasets 3
Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]
Homo sapiens
49 data files
| File | Type | Size |
|---|---|---|
| 2R15_CAGATC_L005_R1_001.fastq.gz | RNA-Seq | 1.1 GB |
| 2R16_CTTGTA_L005_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| 2R17_ACAGTG_L006_R1_001.fastq.gz | RNA-Seq | 1.3 GB |
| 2R18_GCCAAT_L006_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| 2R19_CAGATC_L006_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| 2R20_CTTGTA_L006_R1_001.fastq.gz | RNA-Seq | 1.3 GB |
| 2T15_ATCACG_L002_R1_001.fastq.gz | RNA-Seq | 829.0 MB |
| 2T16_CGATGT_L002_R1_001.fastq.gz | RNA-Seq | 837.1 MB |
| 2T17_TTAGGC_L002_R1_001.fastq.gz | RNA-Seq | 820.7 MB |
| 2T17_TTAGGC_L002_R1_001.fastq.gz | RNA-Seq | 820.7 MB |
| 2T18_TGACCA_L002_R1_001.fastq.gz | RNA-Seq | 888.7 MB |
| 2T19_GCCAAT_L002_R1_001.fastq.gz | RNA-Seq | 836.0 MB |
| 2T20_CTTGTA_L002_R1_001.fastq.gz | RNA-Seq | 741.6 MB |
| 3R15_ACAGTG_L007_R1_001.fastq.gz | RNA-Seq | 1.6 GB |
| 3R16_GCCAAT_L007_R1_001.fastq.gz | RNA-Seq | 1.4 GB |
| 3R17_CAGATC_L007_R1_001.fastq.gz | RNA-Seq | 1.4 GB |
| 3R18_CTTGTA_L007_R1_001.fastq.gz | RNA-Seq | 1.2 GB |
| 3R19_ACAGTG_L008_R1_001.fastq.gz | RNA-Seq | 1.6 GB |
| 3R20_GCCAAT_L008_R1_001.fastq.gz | RNA-Seq | 1.5 GB |
| 3T15_ATCACG_L003_R1_001.fastq.gz | RNA-Seq | 1005.6 MB |
| 3T16_CGATGT_L003_R1_001.fastq.gz | RNA-Seq | 983.5 MB |
| 3T17_TTAGGC_L003_R1_001.fastq.gz | RNA-Seq | 1.0 GB |
| 3T18_TGACCA_L003_R1_001.fastq.gz | RNA-Seq | 989.3 MB |
| 3T19_GCCAAT_L003_R1_001.fastq.gz | RNA-Seq | 1.1 GB |
| 3T20_CTTGTA_L003_R1_001.fastq.gz | RNA-Seq | 993.8 MB |
| SRR3208852_GSM2082509 | RNA-Seq | 829.0 MB |
| SRR3208853_GSM2082510 | RNA-Seq | 837.0 MB |
| SRR3208854_GSM2082511 | RNA-Seq | 820.0 MB |
| SRR3208855_GSM2082512 | RNA-Seq | 888.0 MB |
| SRR3208856_GSM2082513 | RNA-Seq | 835.0 MB |
| SRR3208857_GSM2082514 | RNA-Seq | 741.0 MB |
| SRR3208858_GSM2082515 | RNA-Seq | 1005.0 MB |
| SRR3208859_GSM2082516 | RNA-Seq | 983.0 MB |
| SRR3208860_GSM2082517 | RNA-Seq | 1.0 GB |
| SRR3208861_GSM2082518 | RNA-Seq | 989.0 MB |
| SRR3208862_GSM2082519 | RNA-Seq | 1.1 GB |
| SRR3208863_GSM2082520 | RNA-Seq | 993.0 MB |
| SRR3208864_GSM2082521 | RNA-Seq | 1.1 GB |
| SRR3208865_GSM2082522 | RNA-Seq | 1.2 GB |
| SRR3208866_GSM2082523 | RNA-Seq | 1.3 GB |
| SRR3208867_GSM2082524 | RNA-Seq | 1.2 GB |
| SRR3208868_GSM2082525 | RNA-Seq | 1.2 GB |
| SRR3208869_GSM2082526 | RNA-Seq | 1.3 GB |
| SRR3208870_GSM2082527 | RNA-Seq | 1.6 GB |
| SRR3208871_GSM2082528 | RNA-Seq | 1.4 GB |
| SRR3208872_GSM2082529 | RNA-Seq | 1.4 GB |
| SRR3208873_GSM2082530 | RNA-Seq | 1.2 GB |
| SRR3208874_GSM2082531 | RNA-Seq | 1.6 GB |
| SRR3208875_GSM2082532 | RNA-Seq | 1.5 GB |
Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors
Homo sapiens
Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Treatment]
Homo sapiens
96 data files
| File | Type | Size |
|---|---|---|
| 15AZD_ATCACG_L001_R1_001.fastq.gz | RNA-Seq | 831.4 MB |
| 15AZD_ATCACG_L006_R1_001.fastq.gz | RNA-Seq | 505.7 MB |
| 15AZD_GCCAAT_L005_R1_001.fastq.gz | RNA-Seq | 814.5 MB |
| 15AZD_TGACCA_L008_R1_001.fastq.gz | RNA-Seq | 464.5 MB |
| 15DMSO_ATCACG_L004_R1_001.fastq.gz | RNA-Seq | 822.9 MB |
| 15DMSO_ATCACG_L007_R1_001.fastq.gz | RNA-Seq | 539.0 MB |
| 15DMSO_GCCAAT_L001_R1_001.fastq.gz | RNA-Seq | 692.4 MB |
| 15DMSO_GCCAAT_L006_R1_001.fastq.gz | RNA-Seq | 351.3 MB |
| 15Rapamycin_CGATGT_L004_R1_001.fastq.gz | RNA-Seq | 697.2 MB |
| 15Rapamycin_CGATGT_L007_R1_001.fastq.gz | RNA-Seq | 526.3 MB |
| 15Rapamycin_CTTGTA_L001_R1_001.fastq.gz | RNA-Seq | 869.0 MB |
| 15Rapamycin_CTTGTA_L006_R1_001.fastq.gz | RNA-Seq | 360.6 MB |
| 16AZD_ACTTGA_L007_R1_001.fastq.gz | RNA-Seq | 393.3 MB |
| 16AZD_ACTTGA_L008_R1_001.fastq.gz | RNA-Seq | 416.9 MB |
| 16AZD_TGACCA_L002_R1_001.fastq.gz | RNA-Seq | 630.4 MB |
| 16AZD_TGACCA_L005_R1_001.fastq.gz | RNA-Seq | 986.5 MB |
| 16DMSO_ACAGTG_L008_R1_001.fastq.gz | RNA-Seq | 593.8 MB |
| 16DMSO_CTTGTA_L005_R1_001.fastq.gz | RNA-Seq | 887.2 MB |
| 16DMSO_GCCAAT_L002_R1_001.fastq.gz | RNA-Seq | 689.1 MB |
| 16DMSO_GCCAAT_L007_R1_001.fastq.gz | RNA-Seq | 426.7 MB |
| 16Rapamycin_CAGATC_L008_R1_001.fastq.gz | RNA-Seq | 425.5 MB |
| 16Rapamycin_CTTGTA_L002_R1_001.fastq.gz | RNA-Seq | 651.4 MB |
| 16Rapamycin_CTTGTA_L007_R1_001.fastq.gz | RNA-Seq | 339.6 MB |
| 16Rapamycin_TTAGGC_L005_R1_001.fastq.gz | RNA-Seq | 1010.0 MB |
| 19AZD_ACAGTG_L002_R1_001.fastq.gz | RNA-Seq | 519.5 MB |
| 19AZD_ACTTGA_L003_R1_001.fastq.gz | RNA-Seq | 730.7 MB |
| 19AZD_TGACCA_L006_R1_001.fastq.gz | RNA-Seq | 416.8 MB |
| 19AZD_TTAGGC_L008_R1_001.fastq.gz | RNA-Seq | 473.3 MB |
| 19DMSO_CGATGT_L001_R1_001.fastq.gz | RNA-Seq | 799.5 MB |
| 19DMSO_CGATGT_L006_R1_001.fastq.gz | RNA-Seq | 408.4 MB |
| 19DMSO_GCCAAT_L003_R1_001.fastq.gz | RNA-Seq | 652.8 MB |
| 19DMSO_GCCAAT_L008_R1_001.fastq.gz | RNA-Seq | 443.1 MB |
| 19Rapamycin_CTTGTA_L003_R1_001.fastq.gz | RNA-Seq | 616.5 MB |
| 19Rapamycin_CTTGTA_L008_R1_001.fastq.gz | RNA-Seq | 442.9 MB |
| 19Rapamycin_TTAGGC_L001_R1_001.fastq.gz | RNA-Seq | 1.1 GB |
| 19Rapamycin_TTAGGC_L006_R1_001.fastq.gz | RNA-Seq | 417.4 MB |
| 20AZD_GATCAG_L008_R1_001.fastq.gz | RNA-Seq | 419.9 MB |
| 20AZD_GGCTAC_L004_R1_001.fastq.gz | RNA-Seq | 735.5 MB |
| 20AZD_GGCTAC_L007_R1_001.fastq.gz | RNA-Seq | 403.3 MB |
| 20AZD_TAGCTT_L003_R1_001.fastq.gz | RNA-Seq | 649.8 MB |
| 20DMSO_ACAGTG_L006_R1_001.fastq.gz | RNA-Seq | 439.2 MB |
| 20DMSO_CAGATC_L002_R1_001.fastq.gz | RNA-Seq | 702.8 MB |
| 20DMSO_GATCAG_L007_R1_001.fastq.gz | RNA-Seq | 421.4 MB |
| 20DMSO_GCCAAT_L004_R1_001.fastq.gz | RNA-Seq | 619.5 MB |
| 20Rapamycin_CAGATC_L006_R1_001.fastq.gz | RNA-Seq | 393.3 MB |
| 20Rapamycin_CTTGTA_L004_R1_001.fastq.gz | RNA-Seq | 643.2 MB |
| 20Rapamycin_GATCAG_L003_R1_001.fastq.gz | RNA-Seq | 762.4 MB |
| 20Rapamycin_TAGCTT_L007_R1_001.fastq.gz | RNA-Seq | 416.0 MB |
| SRR3208881_GSM2082533 | RNA-Seq | 831.0 MB |
| SRR3208882_GSM2082534 | RNA-Seq | 814.0 MB |
| SRR3208883_GSM2082535 | RNA-Seq | 505.0 MB |
| SRR3208884_GSM2082536 | RNA-Seq | 464.0 MB |
| SRR3208885_GSM2082537 | RNA-Seq | 692.0 MB |
| SRR3208886_GSM2082538 | RNA-Seq | 822.0 MB |
| SRR3208887_GSM2082539 | RNA-Seq | 351.0 MB |
| SRR3208888_GSM2082540 | RNA-Seq | 539.0 MB |
| SRR3208889_GSM2082541 | RNA-Seq | 868.0 MB |
| SRR3208890_GSM2082542 | RNA-Seq | 697.0 MB |
| SRR3208891_GSM2082543 | RNA-Seq | 360.0 MB |
| SRR3208892_GSM2082544 | RNA-Seq | 526.0 MB |
| SRR3208893_GSM2082545 | RNA-Seq | 630.0 MB |
| SRR3208894_GSM2082546 | RNA-Seq | 986.0 MB |
| SRR3208895_GSM2082547 | RNA-Seq | 393.0 MB |
| SRR3208896_GSM2082548 | RNA-Seq | 416.0 MB |
| SRR3208897_GSM2082549 | RNA-Seq | 689.0 MB |
| SRR3208898_GSM2082550 | RNA-Seq | 887.0 MB |
| SRR3208899_GSM2082551 | RNA-Seq | 426.0 MB |
| SRR3208900_GSM2082552 | RNA-Seq | 593.0 MB |
| SRR3208901_GSM2082553 | RNA-Seq | 651.0 MB |
| SRR3208902_GSM2082554 | RNA-Seq | 1010.0 MB |
| SRR3208903_GSM2082555 | RNA-Seq | 339.0 MB |
| SRR3208904_GSM2082556 | RNA-Seq | 425.0 MB |
| SRR3208905_GSM2082557 | RNA-Seq | 519.0 MB |
| SRR3208906_GSM2082558 | RNA-Seq | 730.0 MB |
| SRR3208907_GSM2082559 | RNA-Seq | 416.0 MB |
| SRR3208908_GSM2082560 | RNA-Seq | 473.0 MB |
| SRR3208909_GSM2082561 | RNA-Seq | 799.0 MB |
| SRR3208910_GSM2082562 | RNA-Seq | 652.0 MB |
| SRR3208911_GSM2082563 | RNA-Seq | 408.0 MB |
| SRR3208912_GSM2082564 | RNA-Seq | 443.0 MB |
| SRR3208913_GSM2082565 | RNA-Seq | 1.1 GB |
| SRR3208914_GSM2082566 | RNA-Seq | 616.0 MB |
| SRR3208915_GSM2082567 | RNA-Seq | 417.0 MB |
| SRR3208916_GSM2082568 | RNA-Seq | 442.0 MB |
| SRR3208917_GSM2082569 | RNA-Seq | 649.0 MB |
| SRR3208918_GSM2082570 | RNA-Seq | 735.0 MB |
| SRR3208919_GSM2082571 | RNA-Seq | 403.0 MB |
| SRR3208920_GSM2082572 | RNA-Seq | 419.0 MB |
| SRR3208921_GSM2082573 | RNA-Seq | 702.0 MB |
| SRR3208922_GSM2082574 | RNA-Seq | 619.0 MB |
| SRR3208923_GSM2082575 | RNA-Seq | 439.0 MB |
| SRR3208924_GSM2082576 | RNA-Seq | 421.0 MB |
| SRR3208925_GSM2082577 | RNA-Seq | 762.0 MB |
| SRR3208926_GSM2082578 | RNA-Seq | 643.0 MB |
| SRR3208927_GSM2082579 | RNA-Seq | 393.0 MB |
| SRR3208928_GSM2082580 | RNA-Seq | 416.0 MB |
Potentially related datasets 3
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
| Accession | Source | Title |
|---|---|---|
| GSE16969 | GSE · GEO GEO ↗ | Gene expression analysis of TSC-tubers reveals increased expression of adhesion and inflammatory factors |
| GSE35338 | GSE · GEO GEO ↗ | Expression data from reactive astrocytes acutely purified from young adult mouse brains |
| GSE78961 | GSE · GEO GEO ↗ | Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors |
Analysis pipelines 5
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE16969 Microarray Data Processing geo_data_processing | Microarray | 2 | GSE16969 |
| GSE35338 Data Processing geo_data_processing | — | 1 | GSE35338 |
| GSE78959 RNA-seq Data Processing geo_data_processing | RNA-seq | 3 | GSE78959 |
| GSE78960 RNA-seq Data Processing geo_data_processing | RNA-seq | 3 | GSE78960 |
| GSE78961 RNA-seq Data Processing geo_data_processing | RNA-seq | 3 | GSE78961 |
Funding 2 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| R01 NS075449 | NINDS NIH HHS (United States) |